The class B airspace used by the three airports is extremely congested. Despite caps placed by the Federal Aviation Administration (FAA) limiting the number of flights per hour, they rank among the top five in the USA for delays. In 2012 travel guide Frommer's rated three terminals in the region as the worst in the world: JFK Terminal 3, Newark Terminal B, and LGA's US Airways terminal. It rated Terminal 5 at JFK the best in the US.[4][5]

In addition to JFK, EWR, and LGA, there are satellite or reliever airports in the metro area which provide additional commercial air carrier service, albeit on a much smaller scale,[6] as well as numerous general aviation airports, heliports, and seaplane bases.

LaGuardia Airport (LGA), the smallest of New York area's primary airports, handles domestic flights. It is named for Fiorello H. LaGuardia, the city's Depression-era mayor known as a reformist and strong supporter of the New Deal. A perimeter rule prohibits incoming and outgoing flights that exceed 1,500 miles (2,400 km) except on Saturdays, when the ban is lifted, and to Denver, Colorado, which has a grandfathered exemption. As a result, most transcontinental and international flights use JFK and Newark (although there are international flights to the Canadian cities of Toronto, Montreal and Ottawa).[16] The airport is located in northern Queens about 6 miles (9.7 km) from downtown Manhattan.

There are numerous heliports located around the New York metro area.[21] Three of the busiest are located in Manhattan:

Downtown Manhattan Heliport, located at the eastern end of Wall Street on Pier 6, on the East River, was the first heliport in the United States to be certified for scheduled passenger helicopter service by the FAA. The heliport was the normal landing spot for US Presidents visiting New York. The soundproof terminal contains gift shops, administrative offices, a VIP lounge and general passenger waiting area, as well as X-ray and bomb-detection machines at a security checkpoint.

East 34th Street Heliport, which consists of a terminal building and fuel filling station and averages 20,000 take-offs and landings each year.

An average of 40% of passenger aircraft delays in the U.S. originated in the New York metropolitan area, some in the area and others due to cascading effects.[23] One-third of aircraft in the national airspace system move through the New York area at some point during a typical day.[24] The three major airports rank among the worst airports for delays the USA despite FAA caps limiting the number of takeoffs and landings per hour to 83 at both JFK and EWR and 71 at LGA.[25] While an increased demand for passengers and freight is foreseen limited land availability in the heavily urbanized area and prohibitive costs constrict expansion of JFK, EWR, and LGA. Approaches to mitigate delays and increase capacity include costly runway expansion projects and greater use of reliever airports. Before the establishment of the Great Swamp National Wildlife Refuge in 1960 the PANYNJ had proposed to build an airport at the location in Morris County, New Jersey but was widely opposed. Studies conducted by the Federal Aviation Authority, the Regional Plan Association, the PANYNJ, and others have identified few sites within the region which would satisfy the requirements for a major airport and evaluated potential dispersion of flights to outlying commercial airports, including Atlantic City International Airport (ACY), Lehigh Valley International Airport (ABE), Bradley International Airport (BDL), and Tweed New Haven Regional Airport (HVN).[26][27][28] In July 2013, the PANYNJ took control of ACY.[29]

Flushing Airport was another early airport in New York City. It opened in 1927 and was the busiest airport in New York for a time. A decade later it was overshadowed by the larger LaGuardia Airport, which is located only a mile away. The airport was decommissioned in 1984 after a fatal accident in 1977. Now the area is wetlands owned by the New York City Economic Development Corporation.

^GAO-08-934T, Statement of Susan Fleming, Director Physical Infrastructure Issues, in Testimony Before the Subcommittee on Aviation Operations, Safety, and Security, Committee on Commerce, Science, and Transportation, U.S. Senate. "NATIONAL AIRSPACE SYSTEM: DOT and FAA Actions Will Likely Have a Limited Effect on Reducing Delays during Summer 2008 Travel Season. July 15, 2008

^"FAA limits at Newark, N.Y. airports have not curbed delays, need to be adjusted, U.S. report shows". The Star-Ledger. November 2, 2010. Retrieved 2012-01-16. Newark and Kennedy takeoffs and landings are limited to 81 an hour from 6 a.m. to 10:59 p.m. daily; LaGuardia flights are restricted to 71 hourly from 6 a.m. to 9:59 p.m. Monday through Friday and from noon to 9:59 p.m. on Sunday. The FAA placed the cap on LaGuardia in 2001 after letting carriers exceed limits the previous year that had been in place since 1968. The FAA extended the LaGuardia cap in 2006 and in 2009 lowered it to 71 from 75.